Reference sequence (1): ORF1AB_China_Dec2019a Identities normalised by aligned length. Colored by: identity |
cov pid 1 [ . . . . : . . . . 1 . . 120 1 ORF1AB_China_Dec2019a 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 17 ORF1AB_China_11Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSEARTAPHGHVMVELVA-----ELEGI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPH-----ELVA-----ELEGI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRS-ARTAPHGHVMVELVA-----ELEGI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 30 ORF1AB_China_08Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 36 ORF1AB_China_02Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% MESLVPGFNEKT----------------HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL----PQLEQPYVFIKRSDARTAPHGHVMVELVA-----ELEGI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% -MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLC--------GSGNLVEKL----SPWFMDGENAY-EVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQL consensus/100% ..ShVsGhstps................HVpLolPlh........G.Gs.VEcl....p.ahhDGpsuh.EV.KuhL....P.L..Phhhht+o.thsuP+.....cLlA......lptl consensus/90% MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRScARTAPHsalh.ELVA.....ELEGI consensus/80% MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRSDARTAPHGHVMVELVA.....ELEGI consensus/70% MESLVPGFNEKT................HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL....PQLEQPYVFIKRSDARTAPHGHVMVELVA.....ELEGI cov pid 121 . . : . . . . 2 . . . . 240 1 ORF1AB_China_Dec2019a 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 17 ORF1AB_China_11Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYG---ADLDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 30 ORF1AB_China_08Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 36 ORF1AB_China_02Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QYGRS-----------GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% AYSSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGR---GGYHY----TPFHYERDNTSCP--EWMDDFEADPKGKYAQNLLKKLIGGDVTP-VDQYMCGVDGKPISAYAFL consensus/100% tYupS...........GcslGhhhPashElssuhpplLLRK.Gp...GGapY....tshchtc-.sosP..-a.-sapsc.puthsppLh+cL.GGshT..VDp.hCGsDGhPlpsht.L consensus/90% QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYG...psFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL consensus/80% QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL consensus/70% QYGRS...........GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDL cov pid 241 : . . . . 3 . . . . : . 360 1 ORF1AB_China_Dec2019a 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 17 ORF1AB_China_11Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 30 ORF1AB_China_08Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 36 ORF1AB_China_02Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LARAGKAS-CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE---CNQMCLSTL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% MAKDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPPHY-FTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAF consensus/100% hA+sGhsp.sslptplshhssccGhhsh+pp.aclsWasERp-hsY.hQo.FpIp.shphDshpspsPpa.FsLsshIhTlpPRschptlssh.h+.+.lYshhu.pp...ss.hhhSsh consensus/90% LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL consensus/80% LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL consensus/70% LARAGKAS.CTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNE...CNQMCLSTL cov pid 361 . . . 4 . . . . : . . . 480 1 ORF1AB_China_Dec2019a 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 7 ORF1a_Finland_29Jan2020 61.9% 73.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRANANIGCN 17 ORF1AB_China_11Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 30 ORF1AB_China_08Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 36 ORF1AB_China_02Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 37 ORF1AB_USA_19Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCP-----ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IECGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSERC-NVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRI consensus/100% hcCspCGpsSW.TGshlpuhsphCGsp.hsp-.tsposGhl..NAllphhCP.....uCpssphts.tpLspYhsEps.psIhcptuhTlhFGGssauYhGCcptshYaVPRApuslup. consensus/90% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRAsANIGCN consensus/80% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN consensus/70% MKCDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCP.....ACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCN cov pid 481 . 5 . . . . : . . . . 6 600 1 ORF1AB_China_Dec2019a 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 7 ORF1a_Finland_29Jan2020 61.9% 73.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 17 ORF1AB_China_11Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 30 ORF1AB_China_08Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 36 ORF1AB_China_02Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% HTGVVGEGSEGLNDNLLEI----LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG----EQKSILSPLYAFA--SEAARVV 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% GDSIF-TGCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKV consensus/100% tsulh.pGspG..splhpI....LpppphslNhVG-FhlN-.lhhILuuhossssthhphlKGlshcth+phltsh.shtVTtG.hhcsAhNlG....p.tuIhuPhhshs..uEuh+hV consensus/90% HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV consensus/80% HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV consensus/70% HTGVVGEGSEGLNDNLLEI....LQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIG....EQKSILSPLYAFA..SEAARVV cov pid 601 . . . . : . . . . 7 . . 720 1 ORF1AB_China_Dec2019a 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 7 ORF1a_Finland_29Jan2020 61.9% 73.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 17 ORF1AB_China_11Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 30 ORF1AB_China_08Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 36 ORF1AB_China_02Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% RSIFSRTLETAQNSVRVLQKAAI------TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% ATIPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCV----DLSVASTYFLVRL---LQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYV consensus/100% toI..+shpospsolphht+usl......sh.sGlSpaS.hLhDsh....DLussshhhhshl...l.phTupahosIhsos.ptlp.lLDhh.EthctshpFLhDhhtlh+hh.psAh. consensus/90% RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE consensus/80% RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE consensus/70% RSIFSRTLETAQNSVRVLQKAAI......TILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACE cov pid 721 . . : . . . . 8 . . . . 840 1 ORF1AB_China_Dec2019a 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 7 ORF1a_Finland_29Jan2020 61.9% 73.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 17 ORF1AB_China_11Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 30 ORF1AB_China_08Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 36 ORF1AB_China_02Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA-LNLGETFVTHSKGLYRKCVKSR-----EETGLLMPLKAPKEIIFL-----EGETLPTEVLTEEVVLKTGDLQPLE 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% YTSQGFVVVNGKVSTLVKQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVTVSSNMVETVVGQLEQTN consensus/100% hsutthVssstclpp.VpphhcLlNKhhtLhtspl.huG.plpA.l..Gcp.lhaspGhYh.CVpo+.....p-hsllhPhchsKc.lhL.....pupTlsspV.op.V.hhsGpLp.hp consensus/90% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE consensus/80% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE consensus/70% IVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKA.LNLGETFVTHSKGLYRKCVKSR.....EETGLLMPLKAPKEIIFL.....EGETLPTEVLTEEVVLKTGDLQPLE cov pid 841 : . . . . 9 . . . . : . 960 1 ORF1AB_China_Dec2019a 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGSAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 17 ORF1AB_China_11Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 30 ORF1AB_China_08Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 36 ORF1AB_China_02Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC--ALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA-YTVELGTEVNEFACVVADAVIKTL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% MHSPDVI----VGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSLSIEEFADVVKEQVSDLL consensus/100% ..os-sl....VGs.VhIsthhhlc.K-p-tas..shssNhhsssshFpLKGuAPs.KVsFGsDpVhEVtuh+SVslpaplcthlDplLspps.t.asV-huhplpEFAsVVt-tV.chL consensus/90% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL consensus/80% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL consensus/70% QPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYC..ALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSA.YTVELGTEVNEFACVVADAVIKTL cov pid 961 . . . 0 . . . . : . . . 1080 1 ORF1AB_China_Dec2019a 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSIATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 7 ORF1a_Finland_29Jan2020 61.9% 73.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 17 ORF1AB_China_11Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQLEEEQEE--DWLDDDSQQTVGQQDGSE 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQ-EEEQEE--DWLDDDSQQTVGQQDGSE 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 30 ORF1AB_China_08Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 36 ORF1AB_China_02Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ---YEYGTED---DYQGKPLEFGATSAALQPEEEQEE--DWLDDDSQQTVGQQDGSE 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% VKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTESVQEEAQPVEVPVEDIA consensus/100% ..l.chhs..shDLD-a..AshYhFstpG-hphuSpMhhShaPs-pDEEpu-sEtp-hE.upp....EhuTEp...saphps.EauAsssth...-EtE-..-.lp--uQ.s.s..-s.t consensus/90% QPVSELLTPLGIDLDEWShATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE consensus/80% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE consensus/70% QPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQ...YEYGTED...DYQGKPLEFGATSAALQPEEEQEE..DWLDDDSQQTVGQQDGSE cov pid 1081 . 1 . . . . : . . . . 2 1200 1 ORF1AB_China_Dec2019a 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 17 ORF1AB_China_11Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 30 ORF1AB_China_08Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 36 ORF1AB_China_02Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% D-------NQTTTIQTIVEVQPQL------EMELTPVVQTI-------------------------EVNSFSGYLK--LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% QVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLVNAANTHLKHGGGIAGAI consensus/100% p.......ppTsslpshVEV.PQl........plpP.Vppl.........................pVsshSsa.+..lT-sVhIh.uDhlp.AKpht.oVlVNAANsaLKHGGGlAGAl consensus/90% D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL consensus/80% D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL consensus/70% D.......NQTTTIQTIVEVQPQL......EMELTPVVQTI.........................EVNSFSGYLK..LTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGAL cov pid 1201 . . . . : . . . . 3 . . 1320 1 ORF1AB_China_Dec2019a 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NKATNNAMQFESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 7 ORF1a_Finland_29Jan2020 61.9% 73.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 17 ORF1AB_China_11Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 30 ORF1AB_China_08Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 36 ORF1AB_China_02Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT-------- 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT-------- 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT-------- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVNSQDVYKSLT-------- consensus/100% NtAopsAhQhESD-YIhspGPLpVGsSslLpGHsLAKphLHVVGPsspttpDlpLLppsYcshNta.lllsPLlSAGIFGscPhhShchhlcps+TpVhlsV.spslYcpLs........ consensus/90% NKATNNAMQhESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS consensus/80% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS consensus/70% NKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKS cov pid 1321 . . : . . . . 4 . . . . 1440 1 ORF1AB_China_Dec2019a 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 7 ORF1a_Finland_29Jan2020 61.9% 73.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 17 ORF1AB_China_11Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 30 ORF1AB_China_08Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 36 ORF1AB_China_02Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------ 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% -------IVDIPQ------------------------------------------------------------------SLTFS------------------------------------ consensus/100% .......Is-IPp..................................................................slTF..................................... consensus/90% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK consensus/80% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK consensus/70% EKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAK cov pid 1441 : . . . . 5 . . . . : . 1560 1 ORF1AB_China_Dec2019a 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 17 ORF1AB_China_11Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 30 ORF1AB_China_08Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 36 ORF1AB_China_02Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY-GARFYFYTSKTTVASL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% -------------YDG-------------------------------------------LRGAIRKAKDYGFTVFVCTDNSANTKVLRNK--GVDYTKKFLTVDGVQYYCYTSKDTLDDI consensus/100% .............YsG...........................................LRthlt+Ac-hthhh.VCs-spA.spslppK..Glchpcthlsh.GspaYhYTSKsTlssl consensus/90% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL consensus/80% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL consensus/70% ALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY.GARFYFYTSKTTVASL cov pid 1561 . . . 6 . . . . : . . . 1680 1 ORF1AB_China_Dec2019a 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 7 ORF1a_Finland_29Jan2020 61.9% 73.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 17 ORF1AB_China_11Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 30 ORF1AB_China_08Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 36 ORF1AB_China_02Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 37 ORF1AB_USA_19Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK-TPEEHFIETISLAGSYKDWSYSG-----QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% LQQANK-SVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAI---LMSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLN-KLLHWSDQTICYKDSVFYVVKNS consensus/100% lpphNc.s.slloMPLGYVoHGLsL.pAuphhRplpVPhss.lus.-t.sh...hhopssK.sPpEcFIcplphsGuYpsWphst.....QshpLs.chL+huDpolhYpssshhhhhsu consensus/90% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG consensus/80% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG consensus/70% INTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSK.TPEEHFIETISLAGSYKDWSYSG.....QSTQLGIEFLKRGDKSVYYTSNPTTFHLDG cov pid 1681 . 7 . . . . : . . . . 8 1800 1 ORF1AB_China_Dec2019a 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 7 ORF1a_Finland_29Jan2020 61.9% 73.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 17 ORF1AB_China_11Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 30 ORF1AB_China_08Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 36 ORF1AB_China_02Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EVITFDNL---KTLLSLREVR--TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV---LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALK--ELYGPVDPTFLHRFYSLKAAVHKWKMVV consensus/100% pshsF-sL...+shLs.Rpsp..TIcVhsTVDslNh+T.Vls.p.TYtpQhGssahsGADlochhPcppppG+ohYl...LssD-Thtlc..EhYtssDPoFLtRahShhsts+KWKhs. consensus/90% EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ consensus/80% EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ consensus/70% EVITFDNL...KTLLSLREVR..TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV...LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQ cov pid 1801 . . . . : . . . . 9 . . 1920 1 ORF1AB_China_Dec2019a 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHXNLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 7 ORF1a_Finland_29Jan2020 61.9% 73.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 17 ORF1AB_China_11Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 30 ORF1AB_China_08Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 36 ORF1AB_China_02Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 37 ORF1AB_USA_19Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% VNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR-VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% CDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVED consensus/100% sstlpSlKhuDNNCYLssslhTLp.l.-lKFs.PALQcAah+t+uG-ussFhALIhAYsNpThGt.sDspchhphlht+.pLssstR.Vhp.hCpsCG.ppssLpGlcAshYhGs.ohEp consensus/90% VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ consensus/80% VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ consensus/70% VNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKR.VLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ cov pid 1921 . . : . . . . 0 . . . . 2040 1 ORF1AB_China_Dec2019a 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 7 ORF1a_Finland_29Jan2020 61.9% 73.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 17 ORF1AB_China_11Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 30 ORF1AB_China_08Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 36 ORF1AB_China_02Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 37 ORF1AB_USA_19Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT---FTCASEYTG-NYQCGHYKHITSKETL-YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% LRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVVRYSLDGNFRTEVD consensus/100% h+tthphsCpCGtptp+.lVpppoPalhhSusPsph.lppuT...Fsshs.apG.phtsGHYhHhp.KtsL.hphDuuhloKoS-aKs.lTDVha.tppYooshpsVpYpLDGshpTElD consensus/90% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID consensus/80% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID consensus/70% FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGT...FTCASEYTG.NYQCGHYKHITSKETL.YCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEID cov pid 2041 : . . . . 1 . . . . : . 2160 1 ORF1AB_China_Dec2019a 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 7 ORF1a_Finland_29Jan2020 61.9% 73.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 17 ORF1AB_China_11Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 30 ORF1AB_China_08Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 36 ORF1AB_China_02Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% PKLDNYYKKDNSYFT-EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD-----LNQLTGYK--KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% PDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILWVNKASYDTNLNKF consensus/100% PcLssaYhKDspYFT.E.PlshsPsp.hssusasN.phVssshp.usD.....hNpLhGac..KPso+chphoFhPc.sGDVlhh-acpYsP.aKpGAhhhtKPIlWhspsuhspsh.K. consensus/90% PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP consensus/80% PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP consensus/70% PKLDNYYKKDNSYFT.EQPIDLVPNQPYPNASFDNFKFVCDNIKFADD.....LNQLTGYK..KPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKP cov pid 2161 . . . 2 . . . . : . . . 2280 1 ORF1AB_China_Dec2019a 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 7 ORF1a_Finland_29Jan2020 61.9% 73.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 17 ORF1AB_China_11Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 30 ORF1AB_China_08Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 36 ORF1AB_China_02Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD--VLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVD-NSSLTIKKPNELSRVLGLKT 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NRASLRQIFDVAPIELENKFTPLSVEST------------PVEPPTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVLKDNVLSSMLRLHT consensus/100% NphslRplasstPlEhpNpFssLpsEss............PVp..sV-ssslQp-..llcCpshsp.hVtD.l.hhssssuh.lsE.lu+pDLhshYVD.p.plhlhKsN.LSphLtL+T consensus/90% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT consensus/80% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT consensus/70% NTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKD..VLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVD.NSSLTIKKPNELSRVLGLKT cov pid 2281 . 3 . . . . : . . . . 4 2400 1 ORF1AB_China_Dec2019a 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRITNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------C-------FTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 17 ORF1AB_China_11Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------C-------FTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 30 ORF1AB_China_08Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 36 ORF1AB_China_02Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LATHGLAAVNSVPWDTIAN--------YAKPFLNKVVSTTTNIVTRCLNRV-------------CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT---IAKNTVKSVGKFCLEASFNY 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% VESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTA-VGSCIKSVVRHLGVTKGILTGCFSFVKMLFMLPLAYFSDSKLGTTEVKVSALKTAGVVTGNVVKQCCTAAVDLSMDK consensus/100% ltotslssVsuss..Thts........YhK.Fhs+shosTTs.VspClppV.............C.......FhL.Lthho.o+.ssoclKsSh.pT...lstNsVKpssphsl-hShsh consensus/90% LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............Chsah.hhFTLLLQLCTFTR.TNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY consensus/80% LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY consensus/70% LATHGLAAVNSVPWDTIAN........YAKPFLNKVVSTTTNIVTRCLNRV.............CTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTT...IAKNTVKSVGKFCLEASFNY cov pid 2401 . . . . : . . . . 5 . . 2520 1 ORF1AB_China_Dec2019a 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 17 ORF1AB_China_11Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 30 ORF1AB_China_08Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 36 ORF1AB_China_02Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN--------------------LGMPSYCTGYREGYLNSTNVTIATYCTG-SIPCSVCLSGLDSLDTYPSLETIQITISSFKW 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% LRRVDWKSTLRLLL-MLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAY-RANSFDVPTFCANRSAMCNWCLISQDSITHYPALKMVQTHLSHYVL consensus/100% L+pssapphlplll.hLhhohsLhS.lYphhshs.lhSs....................LGhsShCsGhtpuY.pusshslsTaCss.Sh.CshCL.u.DSlspYPuLchlQhplSpahh consensus/90% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW consensus/80% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW consensus/70% LKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSN....................LGMPSYCTGYREGYLNSTNVTIATYCTG.SIPCSVCLSGLDSLDTYPSLETIQITISSFKW cov pid 2521 . . : . . . . 6 . . . . 2640 1 ORF1AB_China_Dec2019a 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 7 ORF1a_Finland_29Jan2020 61.9% 73.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIMA-----PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 17 ORF1AB_China_11Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIMA-----PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 30 ORF1AB_China_08Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 36 ORF1AB_China_02Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW------LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWLFTHI----PMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLCYKRNRLTRVEASTVVCGG consensus/100% slshhhhshEhhLAYhLaTphF.hLhLAuhhphFFu.hulah..pSa......hhWLhht.....PhuuhVRMY.hhAshahlhK.Y.HVlsGCpsosChhCYKRNRhTRVEsoTlVsGs consensus/90% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIhsl....PISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV consensus/80% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV consensus/70% DLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSW......LMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGV cov pid 2641 : . . . . 7 . . . . : . 2760 1 ORF1AB_China_Dec2019a 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 7 ORF1a_Finland_29Jan2020 61.9% 73.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKVSLPINVIVFDGK 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 17 ORF1AB_China_11Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 30 ORF1AB_China_08Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 36 ORF1AB_China_02Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR----ANNTKGSLPINVIVFDGK 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% KRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEVCKTTTGIPEYNFIIYDSS consensus/100% +RoFYlhANGGhuFC+hHNWNCVsCDThssGsTFIs-EVApDLohth+RPINsTDpSpYhVDSVTVKpsslph.ac+sGQ.hYERasLstFsNLDpL+....spsTps...hNhIlaDup consensus/90% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK consensus/80% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK consensus/70% RRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLR....ANNTKGSLPINVIVFDGK cov pid 2761 . . . 8 . . . . : . . . 2880 1 ORF1AB_China_Dec2019a 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 7 ORF1a_Finland_29Jan2020 61.9% 73.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 17 ORF1AB_China_11Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 30 ORF1AB_China_08Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 36 ORF1AB_China_02Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR-QGFVDSDVETKDVVECLKLSHQSDIEV 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% DRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% DRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% DRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% DRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVETNEIVDSVQYAHKHDIQI consensus/100% s+spES.A+SAsVYYSQlhCpsILLlDpuLlosVGDSuElAsKMFDuaVNoFsShaNVsh-KLcpLluTAcstlt+ssshcsVLoTFIsAAR..uhV-SDVETp-lV-slphuHppDIpl consensus/90% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV consensus/80% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV consensus/70% SKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR.QGFVDSDVETKDVVECLKLSHQSDIEV cov pid 2881 . 9 . . . . : . . . . 0 3000 1 ORF1AB_China_Dec2019a 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHSIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 7 ORF1a_Finland_29Jan2020 61.9% 73.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 17 ORF1AB_China_11Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 30 ORF1AB_China_08Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 36 ORF1AB_China_02Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGG-----KIVNNW-LKQLIKV 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNVLRDFTLKGYVLA 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNVLRDFTLKGYVLA 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNALRDFTLKGYVLA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGGAPTWFNALRDFTLKGYVLA consensus/100% Ts-ShNNYh.oYsKs-shospDLGuhIDCsAtplNt.Vh+spshAhIWNstsaMpLS-tL++QIR.As+KsNLsF+LTsuphRtssNllos+hs...lhGG.....phlpsa.LKthlhs consensus/90% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV consensus/80% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV consensus/70% TGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGG.....KIVNNW.LKQLIKV cov pid 3001 . . . . : . . . . 1 . . 3120 1 ORF1AB_China_Dec2019a 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 17 ORF1AB_China_11Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 30 ORF1AB_China_08Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 36 ORF1AB_China_02Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR-GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVP-TTLAWVNNQIIFFVSRVFANTGSV consensus/100% TllhhhsAslhYLhhPsasMs.hp.apscIlsaKslDsGlhRDlsssDpCFANKHtsFspWapp+.GGsYsNshsCPLhsAVIst.sGhhlPslP.ThLthsNsphlaFlsRVFussGsl consensus/90% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI consensus/80% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI consensus/70% TLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR.GGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNI cov pid 3121 . . : . . . . 2 . . . . 3240 1 ORF1AB_China_Dec2019a 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% CYTPSKLIEYTDIATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 17 ORF1AB_China_11Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 30 ORF1AB_China_08Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 36 ORF1AB_China_02Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% CYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQEGVCITTNGSWAIFNDHHLNR consensus/100% CYTP.c.I.YpshusSuClLsuECThF+DApG+.sPYCaDssVL.GuhAYpphRPcsRYsLhDGsh.IpFPpshhEuolRlspThsopYCRaGoCEhuptGVCloTsGpWsl.NDaahsh consensus/90% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL consensus/80% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL consensus/70% CYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSL cov pid 3241 : . . . . 3 . . . . : . 3360 1 ORF1AB_China_Dec2019a 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 7 ORF1a_Finland_29Jan2020 61.9% 73.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSYVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 17 ORF1AB_China_11Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYLFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 30 ORF1AB_China_08Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 36 ORF1AB_China_02Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% PGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATFYFTNEPAFIMHVSWYIMFGP consensus/100% PGVaCGsDhlsllpphhssLhQPIshhplosSlVhGhhlshhlThLhYYh.+h+RAFu-Yo.ssshsslhhlhs.hslChsssh.hh.ssYoslYhYhTFYhTN-suFlhHlpWhlMFsP consensus/90% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSaVVAFNTLLFLMSFTVLCLTPVYsFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP consensus/80% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP consensus/70% PGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTP cov pid 3361 . . . 4 . . . . : . . . 3480 1 ORF1AB_China_Dec2019a 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGVMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 17 ORF1AB_China_11Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 30 ORF1AB_China_08Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 36 ORF1AB_China_02Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LVPFWITIAYIICISTKHFYWFFSNYLKRRV-VF-NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNS--LTNDAYSRFLGLFNKYKYFSGAMETAAYREAAACHLAKALQTYSETGSDLLYQP consensus/100% lVPhWhThsYhlshsh+HFaWhhu.a.K++V.VF.sGh..soFp-AA.shFllNK-hYhtLRss..Ls.stYsRaLuLaNKYKYFSGsM-TsuYREAAsCHLAKALpsaSpoGSDlLYQP consensus/90% LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP consensus/80% LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP consensus/70% LVPFWITIAYIICISTKHFYWFFSNYLKRRV.VF.NGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQP cov pid 3481 . 5 . . . . : . . . . 6 3600 1 ORF1AB_China_Dec2019a 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 17 ORF1AB_China_11Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 30 ORF1AB_China_08Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 36 ORF1AB_China_02Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% PNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTV consensus/100% PpsSITSuVLQSGhhKMuaPSGcVEuCMVQVTCGohTLNGLWLDssVaCPRHVhCsu-ph.sPNY-sLLIphoNHsF.VQ...uusspLRVlGHuMQsslLKLpVDsANPpTPtYpFspl consensus/90% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI consensus/80% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI consensus/70% PQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQ...AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI cov pid 3601 . . . . : . . . . 7 . . 3720 1 ORF1AB_China_Dec2019a 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 7 ORF1a_Finland_29Jan2020 61.9% 73.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 17 ORF1AB_China_11Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 30 ORF1AB_China_08Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 36 ORF1AB_China_02Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% KPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTS consensus/100% pPGtsFSVLACYNGpPoGsapssMRPNaTIKGSFLsGSCGSVGash-hsslsFCYMHpMELssGsHsGosh-GshYGsFhD+QstQsthTDphhoVNVlAWLYAAllNGstWFlp..pTo consensus/90% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT consensus/80% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT consensus/70% QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTT cov pid 3721 . . : . . . . 8 . . . . 3840 1 ORF1AB_China_Dec2019a 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 17 ORF1AB_China_11Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFFYE 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 30 ORF1AB_China_08Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 36 ORF1AB_China_02Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LNDFNLVAMKYNY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% VVSFNEWALANQFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVSTYVIILQATKFTLWNYLFE consensus/100% lssFN.hAht.pa.E.lspppVDh...LuspTGlAl.phhhulppLh.sGhpG+pILGSshLEDEFTP.DVshQh.GVshQSuV++shhGTtHWLhhTlloohllllQuTpaoLa.ahaE consensus/90% LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFhYE consensus/80% LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE consensus/70% LNDFNLVAMKYNY.EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYE cov pid 3841 : . . . . 9 . . . . : . 3960 1 ORF1AB_China_Dec2019a 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 7 ORF1a_Finland_29Jan2020 61.9% 73.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 17 ORF1AB_China_11Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 30 ORF1AB_China_08Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 36 ORF1AB_China_02Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVIVVKRLYNPSLSNFALALCSGVMWLYTYSIG consensus/100% sh.h.hh.hlhsh.AFsMhhVKHKHsFLsLFLLPshhslsYhNhVY.Pso.l....htlhsWLs.sss.hpsh+.pDhshYhShsllLllhstRhh.sshuphshsLhsslhhlYph.hG consensus/90% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG consensus/80% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG consensus/70% NAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYG cov pid 3961 . . . 0 . . . . : . . . 4080 1 ORF1AB_China_Dec2019a 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 17 ORF1AB_China_11Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 30 ORF1AB_China_08Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 36 ORF1AB_China_02Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% EA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMTANNLTAPRNSWEAMALNFKL consensus/100% pA.spsIuhhshlholTSsYohsVhssh.LA+shsahhhtYsP.hhlshsplphIhLlYshLGahCTCYFGlFsLLNhhhRhshGVYDahVSTQEFRaMsupsLhsP+NSh-AhtLNhKL consensus/90% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL consensus/80% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL consensus/70% NALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKL cov pid 4081 . 1 . . . . : . . . . 2 4200 1 ORF1AB_China_Dec2019a 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 7 ORF1a_Finland_29Jan2020 61.9% 73.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 17 ORF1AB_China_11Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 30 ORF1AB_China_08Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 36 ORF1AB_China_02Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQATLSEFSHLATFAELEAAQKAY consensus/100% lGlGGpPCIKVAshQSKhoDlKCTSVVLLSVLQQL+lEusS+hWA.CVphHNDILhApDsoEAFEKhVSLhusLhohpGsVDlstLsp-hhDs.usLQAhhSEFSpLsoaAthtsAQcAY consensus/90% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY consensus/80% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY consensus/70% LGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAY cov pid 4201 . . . . : . . . . 3 . . 4320 1 ORF1AB_China_Dec2019a 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 7 ORF1a_Finland_29Jan2020 61.9% 73.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 17 ORF1AB_China_11Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 30 ORF1AB_China_08Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 36 ORF1AB_China_02Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EQAVANGD-SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% QEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIPLCASNKLRVVIPDFTVWNQV consensus/100% ppAhssGD.S..VLKtLpKulNlAKsta-+DtAhtRKLE+MADQAMTpMYKQARuEDK+AKlsSAMQTMLFsMl+KLDNDsLNsIIsNARsGClPLslIPLssusKLhVVIPDassapps consensus/90% EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT consensus/80% EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT consensus/70% EQAVANGD.SEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNT cov pid 4321 . . : . . . . 4 . . . . 4440 1 ORF1AB_China_Dec2019a 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 7 ORF1a_Finland_29Jan2020 61.9% 73.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% CDGTTFIYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 17 ORF1AB_China_11Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 30 ORF1AB_China_08Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 36 ORF1AB_China_02Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN-SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD-- 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD-- 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD-- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% VTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNC-NTSSLAYYEPVQGRKMLMALLSDNAYLKWARVEGKD-- consensus/100% sshsoh.YAuALW-Ip.lsssDscIVp.S-l.hDss.NLsWPLllpshRAs.SAVKLQNNElpPsuL+pMssuAGppQTsC.sssuLAYYpsspGt+hlhALLSD.t.LKWARh.tpD.. consensus/90% CDGTTFsYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT consensus/80% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT consensus/70% CDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRAN.SAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGT cov pid 4441 : . . . . 5 . . . . : . 4560 1 ORF1AB_China_Dec2019a 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESLG 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 7 ORF1a_Finland_29Jan2020 61.9% 73.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 17 ORF1AB_China_11Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 30 ORF1AB_China_08Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 36 ORF1AB_China_02Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% GFVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPESTADQETYG consensus/100% Ghl.sELpPPC+FlhssPKGPcl+YLYFlKsLNNLpRG.VLGplAATVRLQAGssTEhsuNSoVLShssFsVDstKAYhDalsuGGtPlTNCVKMLss+TGTG.AIoVpPEushDQEohG consensus/90% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESaG consensus/80% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG consensus/70% GTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFG cov pid 4561 . . . 6 . . . . : . . . 4680 1 ORF1AB_China_Dec2019a 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 7 ORF1a_Finland_29Jan2020 61.9% 73.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLN----------------------------------------- 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLN----------------------------------------- 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 17 ORF1AB_China_11Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 30 ORF1AB_China_08Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 36 ORF1AB_China_02Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTDVVYRAFDI--YNDKVAGFAK 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFL------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNRVRGSIVNARIEPCSSGLSTDVVFRAFDICNYKAKVAGIGK 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFL------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% GASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLKRVRGSIVNARIEPCSSGLSTDVVFRAFDICNYKAKVAGIGK consensus/100% GASsCLYCRsHI-HPsspGhCchKGKaVQIPspCspDPVGFsLpNTsCsVCthWhGYGCsCDpLRpshL.pucspsFL.......................................... consensus/90% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVpG.lssARlpPCuoGhSTDVVaRAFDI..YpsKVAGhuK consensus/80% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTDVVYRAFDI..YNDKVAGFAK consensus/70% GASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTDVVYRAFDI..YNDKVAGFAK cov pid 4681 . 7 . . . . : . . . . 8 4800 1 ORF1AB_China_Dec2019a 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 17 ORF1AB_China_11Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 30 ORF1AB_China_08Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 36 ORF1AB_China_02Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% YYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQ-NSEVLKAILVKYGCCDVTYFENKLWFDFVE 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% YYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQ-NSEVLKAILVKYGCCDVTYFENKLWFDFVE consensus/100% ........................................................................................................................ consensus/90% ahKTNsCRF.EhD-psphlDSYFVVKRHThpNYphEcphYsLL+DCsAVA.HDFFhFclDtshsPHIsRQRLTcYTMhDLVYALRHFDp.Ns-sLKtILVpYsCCDssYFppK.WaDFVE consensus/80% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE consensus/70% FLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVE cov pid 4801 . . . . : . . . . 9 . . 4920 1 ORF1AB_China_Dec2019a 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 17 ORF1AB_China_11Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 30 ORF1AB_China_08Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 36 ORF1AB_China_02Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIEWPLTEYDFTDYKVQLFEKYF 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIEWPLTEYDFTDYKVQLFEKYF consensus/100% ........................................................................................................................ consensus/90% NPslltVYtpLGERVRQAlLpTVpFCDtMhpAGlVGVLTLDNQDLNGpWYDFGDFl.TpPGSGVslVDSYYShLMPlLohTcsLsAEoHhDsDhsKPhIcWsLhcYDFT-.+lpLF-+YF consensus/80% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF consensus/70% NPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYF cov pid 4921 . . : . . . . 0 . . . . 5040 1 ORF1AB_China_Dec2019a 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 17 ORF1AB_China_11Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 30 ORF1AB_China_08Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 36 ORF1AB_China_02Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% KYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNAFLDLRTSCFSVAALTTGLTF 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% KYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNAFLDLRTSCFSVAALTTGLTF consensus/100% ........................................................................................................................ consensus/90% KYWDQTYHsNCVNChDDRClLHCANFNVLFuhshP.TsFGPlVRKIFVDGVPFVVSsGYHa+ELGlVhN.DVsLHppRLShKELhhYAADPAMHhASuNhhLDhRToCFSVAALTsslsF consensus/80% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF consensus/70% KYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAF cov pid 5041 : . . . . 1 . . . . : . 5160 1 ORF1AB_China_Dec2019a 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 17 ORF1AB_China_11Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 30 ORF1AB_China_08Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 36 ORF1AB_China_02Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% QTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFNKFGKARVYYESMSYQEQDEL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% QTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFNKFGKARVYYESMSYQEQDEL consensus/100% ........................................................................................................................ consensus/90% QTV+PGNFNpDFYDFsVSKGFFKEGSSVpLKHFFFAQDGNAAIoDYsYYpYNLPTMCDI+QhLFshEVVsKYF-hYDGGClNAspVlVNNLDKSAGaPFNKaGKARlYY-SMSYp-QDtL consensus/80% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL consensus/70% QTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDAL cov pid 5161 . . . 2 . . . . : . . . 5280 1 ORF1AB_China_Dec2019a 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 17 ORF1AB_China_11Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 30 ORF1AB_China_08Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 36 ORF1AB_China_02Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% FAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMPNMCRIFASLILARKHGTCCT 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% FAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMPNMCRIFASLILARKHGTCCT consensus/100% ........................................................................................................................ consensus/90% FAhTKRNVIPThTQMNLKYAISAKNRARTVAGVSIhSTMTNRQaHQKhLKShAATRGATsVIGToKFYGGWc.MLKTlYpDV-NPHLMGWDYPKCDRAMPNMhRIhASLlLARKHsTCCo consensus/80% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS consensus/70% FAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCS cov pid 5281 . 3 . . . . : . . . . 4 5400 1 ORF1AB_China_Dec2019a 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 17 ORF1AB_China_11Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 30 ORF1AB_China_08Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 36 ORF1AB_China_02Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYAFLNKHFSMMILSDDGVVCYN 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYAFLNKHFSMMILSDDGVVCYN consensus/100% ........................................................................................................................ consensus/90% hpcRFYRLANECAQVLSEhVhCGGuhYVKPGGTSSGDATTAYANSVFNIhQAsTANVsALhussGNKIsDK.V+shQacLY.slYRspssDscFVscaYAaLpKHFSMMILSDDuVVCaN consensus/80% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN consensus/70% LSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFN cov pid 5401 . . . . : . . . . 5 . . 5520 1 ORF1AB_China_Dec2019a 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 17 ORF1AB_China_11Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 30 ORF1AB_China_08Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 36 ORF1AB_China_02Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 37 ORF1AB_USA_19Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% SDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAYPLTKHEDIEYQNVFWVYLQY 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% SDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAYPLTKHEDIEYQNVFWVYLQY consensus/100% ........................................................................................................................ consensus/90% SsYAupGhlAuIpNFKpsLYYQNNVFMSEAKCWsETDLpKGPHEFCSQHThhlKpGDDhhaLPYPDPSRILuAGCFVDDIVKTDGTLMlERFVSLAIDAYPLTKH.s.EYtsVFalYLQY consensus/80% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY consensus/70% STYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQY cov pid 5521 . . : . . . . 6 . . . . 5640 1 ORF1AB_China_Dec2019a 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 17 ORF1AB_China_11Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 30 ORF1AB_China_08Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 36 ORF1AB_China_02Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 37 ORF1AB_USA_19Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGCGVSDVTKLYLGGMSYFCVDH 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGCGVSDVTKLYLGGMSYFCVDH consensus/100% ........................................................................................................................ consensus/90% IcKLac-LTGHMLD.YSVMLssDNou+aWE.tFYcshYos.TsLQAVGuCVlCpSQTSLRCGsCIRRPFLCCKCCYDHVIuTsHKhVLSVsPYVCNAPGCsVoDVTpLYLGGMSYaChsH consensus/80% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH consensus/70% IRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSH cov pid 5641 : . . . . 7 . . . . : . 5760 1 ORF1AB_China_Dec2019a 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 17 ORF1AB_China_11Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 30 ORF1AB_China_08Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 36 ORF1AB_China_02Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% RPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPPLNRNYVFTGYHITKNSKVQL 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% RPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPPLNRNYVFTGYHITKNSKVQL consensus/100% ........................................................................................................................ consensus/90% +PshSFPLCANG.VFGLYKNhCsGSssls-FNtlATCDWTpuGDYhLANTsTE.LKLFAAETL+ATEEs.K.SYuIATl+Ellu-RpLhLsWEsGKs+PPLNRNYVFTGY+lTKNSKVQl consensus/80% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI consensus/70% KPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQI cov pid 5761 . . . 8 . . . . : . . . 5880 1 ORF1AB_China_Dec2019a 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPILNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 17 ORF1AB_China_11Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 30 ORF1AB_China_08Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 36 ORF1AB_China_02Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% GEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGLAIYYPTARVVYTACSHAAVD 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% GEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGLAIYYPTARVVYTACSHAAVD consensus/100% ........................................................................................................................ consensus/90% GEYhFE+hDYuDAVsY+uoTTYKLsVGDhFVLTSHoVhsLoAPTlVsQE+YV+ITGLYPhlsls-EFuSpVANaQKsGhpKYsTlQGPPGTGKSHFAIGLAlYYPoARlVYTACSHAAVD consensus/80% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD consensus/70% GEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVD cov pid 5881 . 9 . . . . : . . . . 0 6000 1 ORF1AB_China_Dec2019a 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHCVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 17 ORF1AB_China_11Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 30 ORF1AB_China_08Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 36 ORF1AB_China_02Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% ALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRGTLEPENFNSVTRLMCNLGPD 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% ALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRGTLEPENFNSVTRLMCNLGPD consensus/100% ........................................................................................................................ consensus/90% ALCEKAhKYLsIsKCSRIIPA+ARVECaD+FKVNpT.pQYlFsTlNALPEToADIlVhDElSMsTNYDLSllNARl+AKHhVYlGDPAQLPAPRTLLT+GTLEPE.FNSVsRLMpslGPD consensus/80% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD consensus/70% ALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPD cov pid 6001 . . . . : . . . . 1 . . 6120 1 ORF1AB_China_Dec2019a 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 17 ORF1AB_China_11Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 30 ORF1AB_China_08Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 36 ORF1AB_China_02Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDSSQGSEYQYVIFCQTADTAHA 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDSSQGSEYQYVIFCQTADTAHA consensus/100% ........................................................................................................................ consensus/90% hFLuhChRCPtEIVsTVSALVYsNKLhA+K-hSuQCFKhhYKGslTHDsSSAINRPQlshV+pFlTtNPAWpKAVFISPYNSQNAVApphLGLsTQTVDSSQGSEYpYVIFsQTs-TAHu consensus/80% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS consensus/70% MFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHS cov pid 6121 . . : . . . . 2 . . . . 6240 1 ORF1AB_China_Dec2019a 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 17 ORF1AB_China_11Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 30 ORF1AB_China_08Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 36 ORF1AB_China_02Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNYK---LQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRVISRMGFKLDATVPGYPKLFI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNYK---LQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRVISRMGFKLDATVPGYPKLFI consensus/100% ........................................................................................................................ consensus/90% sNlNRFNVAITRAphGILClMospsLa-pLpFTpLphsphp...LQup.VTGLFKDCS+.hoGLpPs.APTalSVDsKaKTps.hss..slPtshsYpRlIShMGFKhshpVsGYPphFI consensus/80% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI consensus/70% CNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFI cov pid 6241 : . . . . 3 . . . . : . 6360 1 ORF1AB_China_Dec2019a 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 7 ORF1a_Finland_29Jan2020 61.9% 73.0% -------------GFAV------------------------------------------------------------------------------------------------------- 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% -------------GFAV------------------------------------------------------------------------------------------------------- 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 17 ORF1AB_China_11Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 30 ORF1AB_China_08Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 36 ORF1AB_China_02Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% TREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTLDKLSDYCTFVCWAHGFELTS 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% TREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTLDKLSDYCTFVCWAHGFELTS consensus/100% ........................................................................................................................ consensus/90% TREEAlRpVRuWIGFDVEGsHAoRpAsGTNlPLQLGFSTGVNhVs.PsGhVDT..ss.hotluA+PPPG-QFKHLlPLMaKGhsWslVRh+IVQMLSDTLcpLSDhssFVhWAHGFELTS consensus/80% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS consensus/70% TREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTS cov pid 6361 . . . 4 . . . . : . . . 6480 1 ORF1AB_China_Dec2019a 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 17 ORF1AB_China_11Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 30 ORF1AB_China_08Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 36 ORF1AB_China_02Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 37 ORF1AB_USA_19Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% ASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDIEYPYISHEKKLNSCCRIVER 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% ASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDIEYPYISHEKKLNSCCRIVER consensus/100% ........................................................................................................................ consensus/90% hpYFsKIG.EppCChCsRRAssaSos.poYACWpHShGaDYVYNPFhlDVQQWGasGNLtoNHDhYCpVHtsAHVASsDAIMTRCLAlHpCFlcRVDWsIEYPhIucEhKlNusCRhVp+ consensus/80% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH consensus/70% MKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQH cov pid 6481 . 5 . . . . : . . . . 6 6600 1 ORF1AB_China_Dec2019a 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTAGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 17 ORF1AB_China_11Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 30 ORF1AB_China_08Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 36 ORF1AB_China_02Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTR---KVQQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGCDGGSLYVNKHAFHTPAYDVS 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTR---KVQQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGCDGGSLYVNKHAFHTPAYDVS consensus/100% ........................................................................................................................ consensus/90% .VV+AALLAspFshlaDIGNPKuI.hVspssV-W+aaDAQPhoc...KlppLFYo.tshus+FssGlCLFWNCNVs+YPsNuIVCRFDTRVhSphNLPGCDGGSLYVNKHAFHTPAaDhS consensus/80% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS consensus/70% MVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKS cov pid 6601 . . . . : . . . . 7 . . 6720 1 ORF1AB_China_Dec2019a 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFIRLQSLENVAFNVVNKGHFDGQQGEVPVSI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 17 ORF1AB_China_11Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 30 ORF1AB_China_08Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 36 ORF1AB_China_02Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% AFVNLKQLPFFYYSDSPCESHGK-QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% AFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITTCNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIAFNVVKQGHFIGVEGELPVAV 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% AFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITACNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIAFNVVKQGHFIGVEGELPVAV consensus/100% ........................................................................................................................ consensus/90% AFhsLK.LPFFYYSsoPCEsHGp.phlpDIDYVPLKSAsCITtCNLGGAVCR+HAsEYR.Yh-AYNhh.uuGFpLWsYKpFDhYNLWsTFh+lQuLENlAFNVVppGHF.G.pGElPVul consensus/80% AFVNLKQLPFFYYSDSPCESHGK.QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI consensus/70% AFVNLKQLPFFYYSDSPCESHGK.QVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSI cov pid 6721 . . : . . . . 8 . . . . 6840 1 ORF1AB_China_Dec2019a 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 17 ORF1AB_China_11Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 30 ORF1AB_China_08Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 36 ORF1AB_China_02Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 37 ORF1AB_USA_19Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% VNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNIC------FDIRDNGSLEKFMSTPNAIFISDR 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% VNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNIC------FDIRDNGSLEKFMSTPNAIFISDR consensus/100% ........................................................................................................................ consensus/90% lNsplaTKssssDlphFENKTTLPsNlAFELaAKRsl+shP-hKlLpNLtsDIshphVlWDYcRss.hthuTIGVCphTDIshpss.sIC......FDhRssGpl-hFhss.NulhIo-t consensus/80% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG consensus/70% INNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG cov pid 6841 : . . . . 9 . . . . : . 6960 1 ORF1AB_China_Dec2019a 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 17 ORF1AB_China_11Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYK-EGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 30 ORF1AB_China_08Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 36 ORF1AB_China_02Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ---FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% KIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHTTLGGLHLLIGLYKKQQEGHI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% KIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHTTLGGLHLLIGLYKKQQEGHI consensus/100% ........................................................................................................................ consensus/90% plKth.s.VGPc.A.hNGshlhspsVhpQ...F.hYKKVss.h.p.sEshaTQSRshp-FhPhSpMEhDFLphs.D.FIc+Yt.EsYAFEHlVYGDFSHopLGGLHLLIGLhK+.pEu.h consensus/80% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ...FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF consensus/70% SVKGLQPSVGPKQASLNGVTLIGEAVKTQ...FNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF cov pid 6961 . . . 0 . . . . : . . . 7080 1 ORF1AB_China_Dec2019a 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 17 ORF1AB_China_11Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 30 ORF1AB_China_08Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 36 ORF1AB_China_02Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% IMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMP 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% IMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMP consensus/100% ........................................................................................................................ consensus/90% .hE-hl.hsSTl+NYFIT-spTuu.KsVCSVIDLhLDDFV.IlKSQDLuVVSKVVKVsIDhT.IpFMLWCKDGpVpTFYP+LQuStsWpPGhAMPsLaKhQph.LE+C-LtNYtpShshP consensus/80% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP consensus/70% ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLP cov pid 7081 . 1 . . . . : . . . . 2 7200 1 ORF1AB_China_Dec2019a 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGMLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 17 ORF1AB_China_11Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 30 ORF1AB_China_08Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 36 ORF1AB_China_02Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ---------------------------------------------------------------------------------------------------------NESGVLL-------- 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% RGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLI 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ---------------------------------------------------------------------------------------------------------NESGVLL-------- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% RGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLI consensus/100% ........................................................................................................................ consensus/90% +GlhMNlAKYhQLCQYLNThTLAVPhNMRVIHFGAGSDKGlAPGTuVLRQWLPTshlllDsDLN-FVSDAD.TLhGDCsTV+supphDLlISDMYDPpTKNVTtpN-SKthFFTYlCshI consensus/80% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI consensus/70% KGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI cov pid 7201 . . . . : . . . . 3 . . 7320 1 ORF1AB_China_Dec2019a 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 7 ORF1a_Finland_29Jan2020 61.9% 73.0% ------------------------------------------------------------------------------------------------------------------------ 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% ------------------------------------------------------------------------------------------------------------------------ 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQINGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 17 ORF1AB_China_11Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 30 ORF1AB_China_08Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 36 ORF1AB_China_02Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% NNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQ 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% ------------------------------------------------------------------------------------------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% NNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQ consensus/100% ........................................................................................................................ consensus/90% pppLALGGSVAIKITEHSWss-LYcLMG+FAWWTsFsTNsNASSSEuFLlGhNYLGp.+EpIsGhsMHANYIFWRNosPhpLSoYSLFDhSKF.LKL+GTsVhpLKEuQIN-hllSLLSp consensus/80% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK consensus/70% QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSK cov pid 7321 . . ] 7346 1 ORF1AB_China_Dec2019a 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 2 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 3 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 4 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 5 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 6 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 7 ORF1a_Finland_29Jan2020 61.9% 73.0% -------------------------- 8 ORF1a_China-Yunnan_17Jan2020 62.1% 73.2% -------------------------- 9 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 10 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 11 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 12 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 13 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 14 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 15 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 16 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 17 ORF1AB_China_11Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 18 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 19 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 20 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 21 ORF1AB_Japan_2020Feb10 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 22 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 23 ORF1AB_USA-CA_27Jan2020 99.9% 99.8% GRLIIRENNRVVISSDVLVNN----- 24 ORF1AB_Finland_29Jan2020 99.8% 99.8% GRLIIRENNRVVISSDVLVNN----- 25 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 26 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 30 ORF1AB_China_08Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 36 ORF1AB_China_02Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GRLIIRENNRVVISSDVLVNN----- 39 ORF1a_MERSctrl_SaudiArabia_01May2013 58.5% 21.1% -------------------------- 40 ORF1AB_MERSctrl_SaudiArabia_01May2013 96.2% 45.0% GKLLIRDNDTLSVSTDVLVNTYRKLR 41 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.5% 21.1% -------------------------- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 96.2% 45.0% GKLLIRDNDTLSVSTDVLVNTYRKLR consensus/100% .......................... consensus/90% G+LlIR-NsplslSoDVLVNs..... consensus/80% GRLIIRENNRVVISSDVLVNN..... consensus/70% GRLIIRENNRVVISSDVLVNN..... |
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